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\name{PROVEANDb-class}
\docType{class}
\alias{PROVEAN}
\alias{PROVEANDb}
\alias{class:PROVEANDb}
\alias{PROVEANDb-class}
\alias{columns,PROVEANDb-method}
\alias{keys,PROVEANDb-method}
\alias{keytypes,PROVEANDb-method}
\alias{select,PROVEANDb-method}
\title{PROVEANDb objects}
\description{
The PROVEANDb class is a container for storing a connection to a PROVEAN
sqlite database.
}
\section{Methods}{
In the code below, \code{x} is a \code{PROVEANDb} object.
\describe{
\item{}{
\code{metadata(x)}:
Returns \code{x}'s metadata in a data frame.
}
\item{}{
\code{columns(x)}:
Returns the names of the \code{columns} that can be used to subset the
data columns.
}
\item{}{
\code{keys(x, keytype="DBSNPID", ...)}:
Returns the names of the \code{keys} that can be used to subset the
data rows. For SIFT.Hsapiens.dbSNP137 the \code{keys} are NCBI dbSNP ids.
}
\item{}{
\code{keytypes(x)}:
Returns the names of the \code{columns} that can be used as \code{keys}.
For SIFT.Hsapiens.dbSNP137 the NCBI dbSNP ids are the only keytype.
}
\item{}{
\code{select(x, keys = NULL, columns = NULL, keytype = "DBSNPID", ...)}:
Returns a subset of data defined by the character vectors \code{keys}
and \code{columns}. If no \code{keys} are supplied, all rows are
returned. If no \code{columns} are supplied, all columns
are returned.
}
}
}
\details{
The SIFT tool is no longer actively maintained. A few of the
orginal authors have started the PROVEAN (Protein Variation
Effect Analyzer) project. PROVEAN is a software tool which predicts
whether an amino acid substitution or indel has an impact on the
biological function of a protein. PROVEAN is useful for filtering
sequence variants to identify nonsynonymous or indel variants that
are predicted to be functionally important.
See the web pages for a complete description of the methods.
\itemize{
\item PROVEAN Home: \url{http://provean.jcvi.org/index.php/}
\item SIFT Home: \url{http://sift.jcvi.org/}
}
Though SIFT is not under active development, the PROVEAN team still
provids the SIFT scores in the pre-computed downloads. This package,
\code{SIFT.Hsapiens.dbSNP137}, contains both SIFT and PROVEAN scores.
One notable difference between this and the previous SIFT database
package is that \code{keys} in \code{SIFT.Hsapiens.dbSNP132} are
rs IDs whereas in \code{SIFT.Hsapiens.dbSNP137} they are NCBI dbSNP IDs.
}
\references{
The PROVEAN tool has replaced SIFT:
\url{http://provean.jcvi.org/about.php}
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the
Functional Effect of Amino Acid Substitutions and Indels.
PLoS ONE 7(10): e46688.
Choi Y (2012) A Fast Computation of Pairwise Sequence Alignment Scores
Between a Protein and a Set of Single-Locus Variants of Another Protein.
In Proceedings of the ACM Conference on Bioinformatics,
Computational Biology and Biomedicine (BCB '12). ACM, New York, NY, USA,
414-417.
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous
variants on protein function using the SIFT algorithm. Nat Protoc.
2009;4(7):1073-81
Ng PC, Henikoff S. Predicting the Effects of Amino Acid Substitutions on
Protein Function Annu Rev Genomics Hum Genet. 2006;7:61-80.
Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein
function. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4.
}
\author{Valerie Obenchain <vobencha@fhcrc.org>}
\examples{
# library(SIFT.Hsapiens.dbSNP137)
#
# ## metadata
# metadata(SIFT.Hsapiens.dbSNP137)
#
# ## keys are the DBSNPID (NCBI dbSNP ID)
# dbsnp <- keys(SIFT.Hsapiens.dbSNP137)
# head(dbsnp)
# columns(SIFT.Hsapiens.dbSNP137)
#
# ## Return all columns. Note that the key, DBSNPID,
# ## is always returned.
# select(SIFT.Hsapiens.dbSNP137, dbsnp[10])
# ## subset on keys and cols
# cols <- c("VARIANT", "PROVEANPRED", "SIFTPRED")
# select(SIFT.Hsapiens.dbSNP137, dbsnp[20:23], cols)
}
\keyword{classes}
\keyword{methods}
|
